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Variant: NM_000162.5(GCK):c.1129C>T (p.Arg377Cys)

CA367398826

585908 (ClinVar)

Gene: GCK
Condition: monogenic diabetes
Inheritance Mode: Semidominant inheritance
UUID: 55dc1eb2-246e-4c40-81d9-6d7af9e62fc4

HGVS expressions

NM_000162.5:c.1129C>T
NM_000162.5(GCK):c.1129C>T (p.Arg377Cys)
NC_000007.14:g.44145621G>A
CM000669.2:g.44145621G>A
NC_000007.13:g.44185220G>A
CM000669.1:g.44185220G>A
NC_000007.12:g.44151745G>A
NG_008847.1:g.48803C>T
NG_008847.2:g.57550C>T
ENST00000395796.8:c.*1127C>T
ENST00000616242.5:c.*249C>T
ENST00000683378.1:n.355C>T
ENST00000336642.9:c.163C>T
ENST00000345378.7:c.1132C>T
ENST00000403799.8:c.1129C>T
ENST00000671824.1:c.1192C>T
ENST00000672743.1:n.141C>T
ENST00000673284.1:c.1129C>T
ENST00000336642.8:c.181C>T
ENST00000345378.6:c.1132C>T
ENST00000395796.7:c.1126C>T
ENST00000403799.7:c.1129C>T
ENST00000437084.1:c.1078C>T
ENST00000459642.1:n.509C>T
ENST00000616242.4:c.1126C>T
NM_000162.3:c.1129C>T
NM_033507.1:c.1132C>T
NM_033508.1:c.1126C>T
NM_000162.4:c.1129C>T
NM_001354800.1:c.1129C>T
NM_001354801.1:c.118C>T
NM_001354802.1:c.-12C>T
NM_001354803.1:c.163C>T
NM_033507.2:c.1132C>T
NM_033508.2:c.1126C>T
NM_033507.3:c.1132C>T
NM_033508.3:c.1126C>T
NM_001354803.2:c.163C>T

Pathogenic

Met criteria codes 6
PS4 PP3 PP2 PP4 PM2_Supporting PS3_Moderate
Not Met criteria codes 1
PP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GCK Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1129C>T variant in the glucokinase gene, GCK, causes an amino acid change of arginine to cysteine at codon 377 (p.(Arg377Cys)) of NM_000162.5. GCK is defined by the ClinGen MDEP VCEP as a gene that has a low rate of benign missense variation and where pathogenic missense variants are a common mechanism of disease (PP2). This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.992, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in at least 7 unrelated individuals with hyperglycemia (PS4; PMID 16731834, 20337973, internal lab contributors). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4; PMID: 20337973). This variant segregated with hyperglycemia with two informative meioses in a single family with diabetes, however, this does not meet the thresholds for PP1 set by the ClinGen MDEP VCEP (PMID: 27236918, internal lab contributors). A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, the wild-type ATP Km is between 0.4-0.65, and the p.Arg377Cys has RAI=0.01, which is less than the MDEP VCEP threshold of 0.50 (PS3_Moderate, PMID: 16731834). In summary, this variant meets the criteria to be classified as pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.2.0, approved 6/7/2023) : PP2, PP3, PM2_Supporting, PS4, PS3_Moderate, PP4.
Met criteria codes
PS4
This variant was identified in at least 7 unrelated individuals with hyperglycemia (PS4; PMIDs: 16731834, 20337973, internal lab contributors).
PP3
This variant is predicted to be deleterious by computational evidence, with a REVEL score of 0.992, which is greater than the MDEP VCEP threshold of 0.70 (PP3).
PP2
GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2).
PP4
This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6%) (PP4; PMID: 20337973).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PS3_Moderate
A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters pass the quality control, the wild-type ATP Km is between 0.4-0.65, and the p.Arg377Cys has RAI=0.01, which is less than the MDEP VCEP threshold of 0.50 (PS3_Moderate, PMID: 16731834).
Not Met criteria codes
PP1
This variant segregated with the disease with two informative meioses in a single family with diabetes, however, this does not meet the thresholds for PP1 set by the ClinGen MDEP VCEP (PMID: 27236918) (internal lab contributors).
Approved on: 2023-08-08
Published on: 2023-08-08
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